Contacts of the helix formed by residues 211 - 218 (chain K) in PDB entry 5XVO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 211 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72K LEU* 3.8 35.4 - - + -
73K PRO* 4.4 5.8 - - + -
184K LEU* 4.1 22.0 - - + -
188K ALA* 3.8 24.0 - - + -
198K THR* 3.3 18.4 - - - -
209K ASN* 3.1 19.3 + - - +
210K ASP* 1.3 89.9 - - + +
212K ASN* 1.3 65.0 + - - +
213K LEU 3.1 3.1 - - - -
214K ALA* 2.9 22.8 + - + -
215K SER* 3.0 11.4 + - - -
81L TYR* 3.5 33.7 - + - -
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Residues in contact with ASN 212 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198K THR 3.2 3.0 + - - -
199K GLN 3.3 22.0 + - - +
200K LEU* 5.0 1.6 - - - +
201K GLY* 3.6 16.9 - - - +
203K LYS 5.8 3.1 - - - +
204K HIS 5.7 1.7 + - - -
208K PHE* 4.4 20.4 - - - +
209K ASN* 3.4 35.0 + - - +
210K ASP 3.7 0.4 - - - -
211K PHE* 1.3 76.5 - - - +
213K LEU* 1.3 56.5 + - - +
215K SER* 3.1 9.9 + - - -
216K ASP* 3.0 31.8 + - - +
87L SER* 5.2 1.6 + - - -
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Residues in contact with LEU 213 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93K GLN* 3.8 14.6 - - - +
96K TRP* 4.2 13.2 - - + -
191K LEU* 3.7 29.1 - - + +
196K CYS* 4.4 2.2 - - + -
197K PHE 3.5 19.1 - - - +
198K THR* 3.0 18.8 + - - +
200K LEU 3.8 9.2 - - - +
201K GLY* 3.8 11.1 - - - -
202K LEU* 3.8 37.2 - - + -
212K ASN* 1.3 74.9 - - - +
214K ALA* 1.3 65.8 + - - +
216K ASP* 3.4 4.5 + - - +
217K LEU* 3.1 28.5 + - + +
276K LEU* 5.4 1.3 - - + -
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Residues in contact with ALA 214 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184K LEU* 3.6 17.7 - - + +
187K PHE* 4.2 4.5 - - + +
188K ALA* 3.8 32.8 - - - +
191K LEU* 3.6 13.4 - - + +
198K THR* 4.3 2.6 + - - -
211K PHE* 2.9 17.0 + - + +
213K LEU* 1.3 77.3 - - - +
215K SER* 1.3 65.1 + - - +
217K LEU* 3.2 2.6 + - - +
218K MET* 3.0 25.3 + - - +
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Residues in contact with SER 215 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184K LEU* 3.7 12.3 - - - +
209K ASN* 3.7 14.4 + - - -
211K PHE 3.0 13.2 + - - -
212K ASN* 3.4 10.7 + - - -
214K ALA* 1.3 76.2 - - - +
216K ASP* 1.3 67.0 + - - +
218K MET* 3.1 26.9 - - - +
219K GLU* 3.3 15.6 - - - +
222K ARG* 4.0 6.5 + - - -
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Residues in contact with ASP 216 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105K TRP* 3.6 28.7 + - + -
108K ILE* 3.5 13.0 - - + +
201K GLY* 3.5 8.3 - - - -
202K LEU* 2.8 44.2 + - + +
203K LYS* 3.8 5.1 + - - +
212K ASN 3.0 12.8 + - - +
213K LEU* 3.5 9.9 - - + +
214K ALA 3.2 0.2 - - - -
215K SER* 1.3 79.6 - - - +
217K LEU* 1.3 63.1 + - + +
219K GLU* 3.2 26.7 + - - +
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Residues in contact with LEU 217 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108K ILE* 4.2 12.8 - - + -
187K PHE* 4.1 12.5 - - + -
191K LEU* 3.8 19.7 - - + -
202K LEU* 4.9 3.6 - - + -
213K LEU* 3.1 26.9 + - + +
214K ALA* 3.2 5.1 + - - +
216K ASP* 1.3 82.5 - - + +
218K MET* 1.3 59.5 + - - +
219K GLU 3.1 1.8 + - - -
220K PRO* 3.4 11.6 - - - +
221K PHE* 4.1 3.6 - - - -
268K TYR* 3.6 17.7 - - + -
269K THR* 3.7 42.8 - - + +
272K VAL* 3.8 33.9 - - + -
273K VAL* 5.4 0.7 - - + -
276K LEU* 5.6 0.9 - - + -
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Residues in contact with MET 218 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180K TYR* 3.5 28.7 - - + +
183K LEU* 3.8 15.0 - - + +
184K LEU* 3.8 34.8 - - - -
187K PHE* 3.7 29.4 - - + -
214K ALA 3.0 11.2 + - - +
215K SER* 3.1 19.1 - - - +
217K LEU* 1.3 76.5 - - - +
219K GLU* 1.3 58.6 + - - +
220K PRO* 3.4 1.8 - - - -
221K PHE* 2.9 25.8 + - - +
222K ARG* 3.5 47.3 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il